No problem - troubleshooting by text is not the easiest thing in the world, beleive me.
There is one issue you should address first, though - when in gear, the bike should be able to be started via pulling the clutch... you state earlier that this does NOT happen, correct?
The clutch perch (assuming it's stock) has a switch that is depressed when the clutch is pulled. It has black/yellow and black wires that lead down to a pair of bullet connectors, also black/yellow and black wires... make sure these are connected. Also, as said earlier, if you plug the harness pair together, the bike will start regardless of being in neutral or pulling the clutch. So, if you can't make it start in gear by pulling the clutch, try connecting them together - will it now start in gear?
If you can get it to the point where it will start in gear, then, when it heats up and won't start (because the nuetral light is off) then it should start either by pulling clutch or by connecting those two clutch switch bullet connectors together. Just more troubleshooting help for when (if) you do get it to fail.
Since you said the neutral light had failed when the no start occurred, and we know the clutch switch isn't working, it would make sense that the bike wouldn't start. BUT now since you have tightened up the neutral switch connection - it is possible that the failure won't occur anymore (in neutral), AND repairing or modding the clutch circuit will make it work even if/when the neutral light is off.